Starting phenix.real_space_refine on Mon May 6 17:11:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsm_18636/05_2024/8qsm_18636.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsm_18636/05_2024/8qsm_18636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsm_18636/05_2024/8qsm_18636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsm_18636/05_2024/8qsm_18636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsm_18636/05_2024/8qsm_18636.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsm_18636/05_2024/8qsm_18636.pdb" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2377 2.51 5 N 573 2.21 5 O 609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 3579 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3579 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 18, 'TRANS': 445} Chain breaks: 3 Time building chain proxies: 2.41, per 1000 atoms: 0.67 Number of scatterers: 3579 At special positions: 0 Unit cell: (80.465, 70.015, 65.835, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 609 8.00 N 573 7.00 C 2377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 819.6 milliseconds 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 846 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 83.4% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 33 through 57 removed outlier: 4.287A pdb=" N ASN A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 70 through 98 removed outlier: 3.899A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 102 through 118 Processing helix chain 'A' and resid 156 through 183 removed outlier: 4.226A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.629A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.818A pdb=" N THR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 246 removed outlier: 3.931A pdb=" N GLY A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 3.638A pdb=" N VAL A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 273 Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.954A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY A 305 " --> pdb=" O MET A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 347 removed outlier: 3.942A pdb=" N VAL A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix removed outlier: 3.691A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 349 No H-bonds generated for 'chain 'A' and resid 348 through 349' Processing helix chain 'A' and resid 365 through 366 No H-bonds generated for 'chain 'A' and resid 365 through 366' Processing helix chain 'A' and resid 367 through 396 removed outlier: 3.958A pdb=" N ASP A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) Proline residue: A 382 - end of helix removed outlier: 5.109A pdb=" N ASP A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Proline residue: A 390 - end of helix Processing helix chain 'A' and resid 400 through 431 removed outlier: 3.528A pdb=" N LYS A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 removed outlier: 4.034A pdb=" N TRP A 453 " --> pdb=" O SER A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 454 through 468 Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 484 through 510 Processing helix chain 'A' and resid 531 through 560 removed outlier: 3.573A pdb=" N HIS A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 439 281 hydrogen bonds defined for protein. 837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1081 1.34 - 1.46: 817 1.46 - 1.58: 1743 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3672 Sorted by residual: bond pdb=" CB PRO A 399 " pdb=" CG PRO A 399 " ideal model delta sigma weight residual 1.492 1.537 -0.045 5.00e-02 4.00e+02 8.11e-01 bond pdb=" CA ILE A 329 " pdb=" C ILE A 329 " ideal model delta sigma weight residual 1.523 1.531 -0.008 9.20e-03 1.18e+04 7.12e-01 bond pdb=" C VAL A 246 " pdb=" O VAL A 246 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 6.67e-01 bond pdb=" CB PRO A 306 " pdb=" CG PRO A 306 " ideal model delta sigma weight residual 1.492 1.524 -0.032 5.00e-02 4.00e+02 4.05e-01 bond pdb=" N VAL A 322 " pdb=" CA VAL A 322 " ideal model delta sigma weight residual 1.463 1.470 -0.007 1.18e-02 7.18e+03 4.00e-01 ... (remaining 3667 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.07: 97 107.07 - 113.80: 2051 113.80 - 120.53: 1489 120.53 - 127.26: 1307 127.26 - 133.99: 41 Bond angle restraints: 4985 Sorted by residual: angle pdb=" C PHE A 247 " pdb=" N ILE A 248 " pdb=" CA ILE A 248 " ideal model delta sigma weight residual 121.97 125.78 -3.81 1.80e+00 3.09e-01 4.48e+00 angle pdb=" N ILE A 466 " pdb=" CA ILE A 466 " pdb=" C ILE A 466 " ideal model delta sigma weight residual 113.00 110.27 2.73 1.30e+00 5.92e-01 4.42e+00 angle pdb=" N GLU A 309 " pdb=" CA GLU A 309 " pdb=" C GLU A 309 " ideal model delta sigma weight residual 110.80 115.23 -4.43 2.13e+00 2.20e-01 4.32e+00 angle pdb=" C THR A 308 " pdb=" N GLU A 309 " pdb=" CA GLU A 309 " ideal model delta sigma weight residual 121.54 125.26 -3.72 1.91e+00 2.74e-01 3.79e+00 angle pdb=" N ALA A 468 " pdb=" CA ALA A 468 " pdb=" C ALA A 468 " ideal model delta sigma weight residual 111.02 113.92 -2.90 1.52e+00 4.33e-01 3.64e+00 ... (remaining 4980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.62: 1970 14.62 - 29.24: 99 29.24 - 43.87: 29 43.87 - 58.49: 8 58.49 - 73.11: 2 Dihedral angle restraints: 2108 sinusoidal: 785 harmonic: 1323 Sorted by residual: dihedral pdb=" CA THR A 308 " pdb=" C THR A 308 " pdb=" N GLU A 309 " pdb=" CA GLU A 309 " ideal model delta harmonic sigma weight residual -180.00 -163.82 -16.18 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ARG A 33 " pdb=" CB ARG A 33 " pdb=" CG ARG A 33 " pdb=" CD ARG A 33 " ideal model delta sinusoidal sigma weight residual -60.00 -115.47 55.47 3 1.50e+01 4.44e-03 9.35e+00 dihedral pdb=" CA ARG A 104 " pdb=" CB ARG A 104 " pdb=" CG ARG A 104 " pdb=" CD ARG A 104 " ideal model delta sinusoidal sigma weight residual 180.00 127.75 52.25 3 1.50e+01 4.44e-03 9.10e+00 ... (remaining 2105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 389 0.025 - 0.050: 100 0.050 - 0.075: 55 0.075 - 0.101: 24 0.101 - 0.126: 6 Chirality restraints: 574 Sorted by residual: chirality pdb=" CA THR A 176 " pdb=" N THR A 176 " pdb=" C THR A 176 " pdb=" CB THR A 176 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE A 439 " pdb=" N ILE A 439 " pdb=" C ILE A 439 " pdb=" CB ILE A 439 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ILE A 435 " pdb=" N ILE A 435 " pdb=" C ILE A 435 " pdb=" CB ILE A 435 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.12e-01 ... (remaining 571 not shown) Planarity restraints: 611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 238 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C VAL A 238 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL A 238 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 239 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 239 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C VAL A 239 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL A 239 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 240 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 237 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C PHE A 237 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE A 237 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 238 " -0.009 2.00e-02 2.50e+03 ... (remaining 608 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 887 2.80 - 3.32: 3828 3.32 - 3.85: 5935 3.85 - 4.37: 6627 4.37 - 4.90: 11289 Nonbonded interactions: 28566 Sorted by model distance: nonbonded pdb=" O LEU A 264 " pdb=" OG SER A 267 " model vdw 2.269 2.440 nonbonded pdb=" O ILE A 461 " pdb=" OG SER A 464 " model vdw 2.272 2.440 nonbonded pdb=" OG1 THR A 333 " pdb=" O GLY A 499 " model vdw 2.305 2.440 nonbonded pdb=" O LYS A 262 " pdb=" OG1 THR A 265 " model vdw 2.316 2.440 nonbonded pdb=" O CYS A 242 " pdb=" OG SER A 245 " model vdw 2.326 2.440 ... (remaining 28561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.910 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.960 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 3672 Z= 0.125 Angle : 0.482 5.910 4985 Z= 0.259 Chirality : 0.034 0.126 574 Planarity : 0.004 0.029 611 Dihedral : 10.371 73.110 1262 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.75 % Allowed : 6.17 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.41), residues: 456 helix: 2.29 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -1.69 (0.60), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 332 HIS 0.001 0.000 HIS A 348 PHE 0.009 0.001 PHE A 198 TYR 0.006 0.001 TYR A 52 ARG 0.001 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6378 (mtm-85) REVERT: A 47 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8512 (tm-30) REVERT: A 91 PHE cc_start: 0.8867 (m-80) cc_final: 0.8633 (m-10) REVERT: A 198 PHE cc_start: 0.9093 (t80) cc_final: 0.8810 (t80) REVERT: A 200 TRP cc_start: 0.9106 (t60) cc_final: 0.8447 (t60) REVERT: A 313 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8762 (mm-30) REVERT: A 342 TYR cc_start: 0.8881 (m-10) cc_final: 0.8544 (m-80) REVERT: A 369 LEU cc_start: 0.8694 (mt) cc_final: 0.8279 (mt) REVERT: A 427 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8142 (mt) REVERT: A 451 LEU cc_start: 0.9317 (tp) cc_final: 0.9072 (mp) REVERT: A 454 GLN cc_start: 0.8734 (tp40) cc_final: 0.8242 (tp40) REVERT: A 457 GLN cc_start: 0.7944 (pt0) cc_final: 0.6272 (pt0) REVERT: A 474 GLU cc_start: 0.8871 (mt-10) cc_final: 0.7895 (mt-10) REVERT: A 535 TYR cc_start: 0.8767 (t80) cc_final: 0.8253 (t80) outliers start: 14 outliers final: 3 residues processed: 181 average time/residue: 0.1716 time to fit residues: 36.8732 Evaluate side-chains 105 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 427 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 345 GLN ** A 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3672 Z= 0.199 Angle : 0.705 9.747 4985 Z= 0.331 Chirality : 0.040 0.154 574 Planarity : 0.005 0.057 611 Dihedral : 5.656 54.530 502 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.29 % Allowed : 18.50 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.40), residues: 456 helix: 2.36 (0.27), residues: 364 sheet: None (None), residues: 0 loop : -1.59 (0.59), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 69 HIS 0.002 0.001 HIS A 395 PHE 0.033 0.002 PHE A 417 TYR 0.013 0.002 TYR A 477 ARG 0.007 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6534 (ptp-170) REVERT: A 91 PHE cc_start: 0.8909 (m-80) cc_final: 0.8680 (m-10) REVERT: A 200 TRP cc_start: 0.9088 (t60) cc_final: 0.8421 (t60) REVERT: A 235 LEU cc_start: 0.9562 (mt) cc_final: 0.8982 (tp) REVERT: A 301 MET cc_start: 0.5921 (tpt) cc_final: 0.5630 (tmm) REVERT: A 331 TYR cc_start: 0.8990 (t80) cc_final: 0.8553 (t80) REVERT: A 427 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8520 (mt) REVERT: A 535 TYR cc_start: 0.8965 (t80) cc_final: 0.8503 (t80) outliers start: 16 outliers final: 9 residues processed: 115 average time/residue: 0.1071 time to fit residues: 16.2111 Evaluate side-chains 100 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 532 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 0.0000 chunk 31 optimal weight: 1.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3672 Z= 0.178 Angle : 0.683 11.474 4985 Z= 0.324 Chirality : 0.039 0.158 574 Planarity : 0.005 0.049 611 Dihedral : 5.748 54.975 500 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.56 % Allowed : 21.72 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.40), residues: 456 helix: 2.17 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.76 (0.66), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 69 HIS 0.001 0.000 HIS A 521 PHE 0.046 0.002 PHE A 372 TYR 0.016 0.002 TYR A 335 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.405 Fit side-chains REVERT: A 33 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6547 (ptp-170) REVERT: A 91 PHE cc_start: 0.8880 (m-80) cc_final: 0.8680 (m-10) REVERT: A 200 TRP cc_start: 0.9125 (t60) cc_final: 0.8436 (t60) REVERT: A 301 MET cc_start: 0.6265 (tpt) cc_final: 0.6008 (tmm) REVERT: A 307 PHE cc_start: 0.3792 (OUTLIER) cc_final: 0.3516 (m-80) REVERT: A 331 TYR cc_start: 0.9072 (t80) cc_final: 0.8671 (t80) REVERT: A 413 MET cc_start: 0.8905 (tmm) cc_final: 0.8593 (tmm) REVERT: A 427 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8618 (mt) REVERT: A 458 TYR cc_start: 0.9052 (m-80) cc_final: 0.8795 (m-80) REVERT: A 535 TYR cc_start: 0.8992 (t80) cc_final: 0.8600 (t80) outliers start: 17 outliers final: 10 residues processed: 108 average time/residue: 0.1124 time to fit residues: 15.9046 Evaluate side-chains 108 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 532 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 0.0870 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3672 Z= 0.174 Angle : 0.691 12.861 4985 Z= 0.328 Chirality : 0.040 0.183 574 Planarity : 0.004 0.036 611 Dihedral : 5.940 58.899 500 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.02 % Allowed : 22.52 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.41), residues: 456 helix: 2.02 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -1.75 (0.68), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 368 HIS 0.001 0.000 HIS A 559 PHE 0.059 0.002 PHE A 372 TYR 0.015 0.001 TYR A 477 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 0.348 Fit side-chains REVERT: A 33 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6457 (ptp-170) REVERT: A 44 GLU cc_start: 0.9315 (tp30) cc_final: 0.9108 (tp30) REVERT: A 48 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8913 (mmp-170) REVERT: A 91 PHE cc_start: 0.8876 (m-80) cc_final: 0.8657 (m-10) REVERT: A 200 TRP cc_start: 0.9149 (t60) cc_final: 0.8472 (t60) REVERT: A 307 PHE cc_start: 0.3755 (OUTLIER) cc_final: 0.3464 (m-80) REVERT: A 331 TYR cc_start: 0.9109 (t80) cc_final: 0.8732 (t80) REVERT: A 413 MET cc_start: 0.8950 (tmm) cc_final: 0.8670 (tmm) REVERT: A 427 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8625 (mt) REVERT: A 458 TYR cc_start: 0.8949 (m-80) cc_final: 0.8730 (m-80) REVERT: A 535 TYR cc_start: 0.8957 (t80) cc_final: 0.8604 (t80) outliers start: 15 outliers final: 8 residues processed: 114 average time/residue: 0.1130 time to fit residues: 16.7349 Evaluate side-chains 107 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3672 Z= 0.178 Angle : 0.673 10.003 4985 Z= 0.321 Chirality : 0.040 0.155 574 Planarity : 0.004 0.042 611 Dihedral : 5.994 59.318 500 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.43 % Allowed : 24.13 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.41), residues: 456 helix: 2.11 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -1.91 (0.68), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 368 HIS 0.002 0.000 HIS A 303 PHE 0.049 0.002 PHE A 372 TYR 0.015 0.001 TYR A 444 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6514 (ptp-170) REVERT: A 44 GLU cc_start: 0.9326 (tp30) cc_final: 0.9122 (tp30) REVERT: A 48 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8913 (mmp-170) REVERT: A 91 PHE cc_start: 0.8885 (m-80) cc_final: 0.8676 (m-10) REVERT: A 200 TRP cc_start: 0.9177 (t60) cc_final: 0.8442 (t60) REVERT: A 220 VAL cc_start: 0.7484 (OUTLIER) cc_final: 0.7283 (m) REVERT: A 331 TYR cc_start: 0.9193 (t80) cc_final: 0.8790 (t80) REVERT: A 427 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8647 (mt) REVERT: A 535 TYR cc_start: 0.9011 (t80) cc_final: 0.8689 (t80) outliers start: 24 outliers final: 10 residues processed: 113 average time/residue: 0.1249 time to fit residues: 18.0219 Evaluate side-chains 105 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3672 Z= 0.169 Angle : 0.709 12.005 4985 Z= 0.324 Chirality : 0.040 0.163 574 Planarity : 0.004 0.037 611 Dihedral : 5.990 58.309 500 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.90 % Allowed : 25.20 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.41), residues: 456 helix: 2.16 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -2.08 (0.68), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 332 HIS 0.001 0.000 HIS A 303 PHE 0.050 0.001 PHE A 372 TYR 0.014 0.001 TYR A 477 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.465 Fit side-chains REVERT: A 33 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6449 (ptp-170) REVERT: A 48 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8913 (mmp-170) REVERT: A 91 PHE cc_start: 0.8876 (m-80) cc_final: 0.8618 (m-10) REVERT: A 200 TRP cc_start: 0.9169 (t60) cc_final: 0.8399 (t60) REVERT: A 331 TYR cc_start: 0.9187 (t80) cc_final: 0.8848 (t80) REVERT: A 371 MET cc_start: 0.8880 (mtt) cc_final: 0.8391 (mmm) REVERT: A 427 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8620 (mt) REVERT: A 457 GLN cc_start: 0.7784 (mp10) cc_final: 0.7545 (mp10) REVERT: A 535 TYR cc_start: 0.8983 (t80) cc_final: 0.8655 (t80) outliers start: 22 outliers final: 11 residues processed: 114 average time/residue: 0.1198 time to fit residues: 17.7555 Evaluate side-chains 106 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.0070 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 0.0470 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3672 Z= 0.167 Angle : 0.769 13.972 4985 Z= 0.339 Chirality : 0.041 0.221 574 Planarity : 0.004 0.040 611 Dihedral : 6.018 57.554 500 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.02 % Allowed : 27.61 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.41), residues: 456 helix: 2.05 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -2.13 (0.67), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 332 HIS 0.000 0.000 HIS A 521 PHE 0.048 0.002 PHE A 372 TYR 0.015 0.001 TYR A 477 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6498 (ptp-170) REVERT: A 110 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9415 (tt) REVERT: A 200 TRP cc_start: 0.9112 (t60) cc_final: 0.8437 (t60) REVERT: A 331 TYR cc_start: 0.9169 (t80) cc_final: 0.8824 (t80) REVERT: A 371 MET cc_start: 0.8877 (mtt) cc_final: 0.8414 (mmm) REVERT: A 427 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8488 (mt) REVERT: A 458 TYR cc_start: 0.8839 (m-80) cc_final: 0.8594 (m-80) REVERT: A 535 TYR cc_start: 0.8951 (t80) cc_final: 0.8663 (t80) outliers start: 15 outliers final: 11 residues processed: 109 average time/residue: 0.1237 time to fit residues: 17.3610 Evaluate side-chains 109 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3672 Z= 0.204 Angle : 0.761 12.216 4985 Z= 0.342 Chirality : 0.040 0.158 574 Planarity : 0.004 0.041 611 Dihedral : 6.019 56.850 500 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.09 % Allowed : 26.81 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.41), residues: 456 helix: 2.08 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -2.18 (0.67), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 332 HIS 0.001 0.000 HIS A 348 PHE 0.040 0.001 PHE A 372 TYR 0.015 0.001 TYR A 477 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6841 (mtt180) REVERT: A 48 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8914 (mmp-170) REVERT: A 200 TRP cc_start: 0.9157 (t60) cc_final: 0.8413 (t60) REVERT: A 371 MET cc_start: 0.8807 (mtt) cc_final: 0.8345 (mmp) REVERT: A 474 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8305 (mt-10) REVERT: A 535 TYR cc_start: 0.8988 (t80) cc_final: 0.8764 (t80) outliers start: 19 outliers final: 12 residues processed: 110 average time/residue: 0.1186 time to fit residues: 16.9603 Evaluate side-chains 103 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3672 Z= 0.209 Angle : 0.810 12.059 4985 Z= 0.362 Chirality : 0.042 0.263 574 Planarity : 0.004 0.040 611 Dihedral : 5.839 54.220 500 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.75 % Allowed : 28.42 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.41), residues: 456 helix: 2.02 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -2.13 (0.68), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 332 HIS 0.001 0.000 HIS A 348 PHE 0.037 0.002 PHE A 372 TYR 0.018 0.001 TYR A 215 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6852 (mtt180) REVERT: A 172 LYS cc_start: 0.9256 (mmmt) cc_final: 0.8976 (mmmt) REVERT: A 200 TRP cc_start: 0.9092 (t60) cc_final: 0.8418 (t60) REVERT: A 331 TYR cc_start: 0.9206 (t80) cc_final: 0.8967 (t80) REVERT: A 371 MET cc_start: 0.8787 (mtt) cc_final: 0.8512 (mtt) REVERT: A 427 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8490 (mt) REVERT: A 454 GLN cc_start: 0.8903 (tp40) cc_final: 0.8618 (tp40) REVERT: A 474 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8122 (mt-10) REVERT: A 489 MET cc_start: 0.9481 (tpp) cc_final: 0.9058 (tpp) outliers start: 14 outliers final: 11 residues processed: 104 average time/residue: 0.1299 time to fit residues: 17.1253 Evaluate side-chains 100 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 0.0970 chunk 33 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3672 Z= 0.196 Angle : 0.820 11.767 4985 Z= 0.370 Chirality : 0.043 0.251 574 Planarity : 0.005 0.040 611 Dihedral : 5.639 54.066 499 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.95 % Allowed : 28.42 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.41), residues: 456 helix: 1.92 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -2.15 (0.69), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 332 HIS 0.001 0.000 HIS A 348 PHE 0.041 0.002 PHE A 372 TYR 0.025 0.001 TYR A 477 ARG 0.002 0.000 ARG A 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6859 (mtt180) REVERT: A 172 LYS cc_start: 0.9246 (mmmt) cc_final: 0.8972 (mmmt) REVERT: A 200 TRP cc_start: 0.9093 (t60) cc_final: 0.8452 (t60) REVERT: A 331 TYR cc_start: 0.9163 (t80) cc_final: 0.8944 (t80) REVERT: A 371 MET cc_start: 0.8747 (mtt) cc_final: 0.8375 (mmm) REVERT: A 427 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8390 (mt) REVERT: A 535 TYR cc_start: 0.8960 (t80) cc_final: 0.8745 (t80) outliers start: 11 outliers final: 9 residues processed: 103 average time/residue: 0.1281 time to fit residues: 16.8439 Evaluate side-chains 100 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 37 optimal weight: 0.2980 chunk 4 optimal weight: 0.4980 chunk 6 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.096437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.081823 restraints weight = 13166.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.083961 restraints weight = 7685.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.085455 restraints weight = 5214.762| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3672 Z= 0.201 Angle : 0.841 11.787 4985 Z= 0.381 Chirality : 0.043 0.199 574 Planarity : 0.005 0.039 611 Dihedral : 5.673 54.226 499 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.49 % Allowed : 28.69 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.41), residues: 456 helix: 1.92 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -2.22 (0.69), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 332 HIS 0.002 0.000 HIS A 395 PHE 0.052 0.002 PHE A 372 TYR 0.015 0.001 TYR A 477 ARG 0.003 0.000 ARG A 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1161.21 seconds wall clock time: 21 minutes 50.64 seconds (1310.64 seconds total)